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10 protocols using zinc formal fixx

1

Tissue Fixation and Staining

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Freshly dissected tissues were rinsed with PBS and fixed with 1× Zinc Formal-Fixx (Thermo Fisher Scientific). Fixed tissues were then dehydrated with ethanol and embedded in paraffin (Surgipath Paraplast Plus, Leica Biosystems Division of Leica, Buffalo Grove, IL, USA). Blocks were sliced into 4 μm sections and stained with H&E (hematoxylin and eosin) and alcian blue solution (pH 2.5).
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2

Collagen and α-SMA Quantification in HUAFs

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HUAFs were cultured on coverslips and transfected with GM-ctrl or GM-113-6 for 24 h. For collagen staining, cells were fixed in Zinc Formal-Fixx (Thermo Fisher Scientific, cat. no. 6764255) for 30 min and washed with PBS. Collagen was visualized with a picrosirius red staining.
For αSMA staining, cells were fixed in 4% PFA for 15 min and washed in PBS. An antibody against αSMA, 1A4 (Dako M0851, 1:1000), and a secondary antibody Alexa Fluor 555 DαMouse (Invitrogen A31570, 1:1000) were used to visualize αSMA. Hoechst (34580, 1:1,000) was used to stain the nuclei.
Fiji was used to perform immunohistochemistry and immunofluorescence analysis. The area was divided by the total amount of nuclei. The integrated density, which is the sum of values of the pixels, was calculated and divided by the total amount of nuclei (intensity).
Primer sequences for COL1A1 and αSMA (smooth muscle α-2 actin [ACTA2]) are provided in Table S1.
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3

Paraffin-Embedded Liver Tissue Immunohistochemistry

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Mouse liver samples were fixed in zinc formal‐fixx (ThermoFisher Scientific) and embedded in paraffin. Hematoxylin (ThermoFisher Scientific) and eosin (ThermoFisher Scientific; H&E) stained slides were used for histology evaluation. Immunohistochemistry was performed as described previously.13 In brief, slides were deparaffinized in xylene, rehydrated through a graded alcohol series and finally, rinsed in PBS. Antigen unmasking was performed via boiling the slides in 0.01 mol/L citrate buffer (pH 6.0) for 10 minutes. The slides were first incubated with 5% goat serum and Avidin‐Biotin Blocking Kit (Vector Laboratories, Burlingame, CA, USA); and, subsequently, with primary antibodies at 4°C for 16 hours. After washing, slides were incubated with 3% hydrogen peroxide for 10 minutes followed by incubating with biotin conjugated secondary antibody for additional 30 minutes at room temperature. Vectastain ABC Elite Kit (Vector Laboratories) was used to visualize the signal. Finally, slides were counterstained with Hematoxylin. Slides incubated without primary antibodies were used as negative control. Images were taken using bright‐field microscope with Digital color camera (Model# DFC295; Leica, San Francisco, CA, USA). Detailed information for the reagents could be found in Table S1 and antibody information in Table S2.
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4

Coral Gametogenesis Transcriptome Analysis

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E. ancora specimens were collected by scuba divers at Nanwan Bay, Kenting National Park, in southern Taiwan (21°57′N, 120°46′E). Approximately 10 colonies were labeled, and gonads (> 20 gonads) of labeled colonies were microscopically isolated at different times during a 9-month period from October 2016 (non-spawning period) to June 2017 (spawning period) (Fig. 1d). Collection was approved by the administrative office of Kenting National Park (issue number: 1010006545). For RNA-seq, collected samples were snap frozen in liquid nitrogen, and stored at − 80 °C until use. Some of the isolated gonads were also fixed with 20% Zinc-Formal-Fixx (Thermo Fisher Scientific, Pittsburgh, PA, USA) for histological analysis. Experiments were performed in accordance with principles and procedures approved by the Institutional Animal Care and Use Committee, National Taiwan Ocean University, Taiwan.
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5

Histological Examination of Heart Tissues

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The dissected hearts were rinsed and fixed with Zinc Formal-Fixx (Thermo Fisher Scientific, Waltham, MA, USA). The fixed heart tissues were dehydrated with several degrees of ethanol and embedded in paraffin. H&E staining was performed, and Masson’s trichrome staining was performed using a Masson’s trichrome stain kit (Polysciences, Inc., Warrington, PA, USA). Oil red O staining was performed as previously described [71 (link)].
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6

Immunohistochemical Analysis of Brown and White Adipose Tissue

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BAT and WAT samples were fixed in 10 ml Zinc Formal Fixx (Thermo Fisher Scientific) during 24 hr at 4°C. Samples were dehydrated using the Leica TP1020 semi-enclosed processor and embedded in paraffin. 6 μm sections were processed for immunohistochemistry (IHC) and EdU detection. Tissue sections from different mice were assayed on the same slide to minimize staining variability.
For IHC, deparaffinized sections were incubated overnight at 4°C with rabbit poly-clonal antibodies directed against UCP1 (Abcam, ab10983), diluted 1:400 in phosphate-buffered saline (PBS)/2.5% goat serum. Sections were then incubated with a horseradish peroxidase-labeled anti-rabbit antibody (1:300, Promega, W401B) for 1 hr at room temperature. Peroxidase activity was visualized with diaminobenzidine staining (Sigma-Aldrich, D5905). Images were acquired using an AxioObserver Zeiss microscope at a ×16 magnification.
EdU detection was assessed as recommended by the manufacturer (Click-iT EdU Cell Proliferation Kit, Thermo Fisher), following deparaffinization of BAT sections. Images were acquired on a DM6000 Leica microscope. Both EdU-positive cells and DAPI (4’,6-diamidino-2-phenylindol)-marked nuclei were quantified on pictures of whole BAT sections to avoid any bias of field selection.
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7

Euthanasia, Bone Dissection, and Decalcification

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The animals were euthanized with an overdose of pentobarbital (150 mg/kg intraperitoneally) after 8 weeks. The animal femurs were dissected free and all bones were examined macro- and microscopically for signs of infection or tumors. Bones were then frozen and stored at −80°C until preparation for immunhistological examinations. Thereafter, the bones were fixed in Zinc-Formal-Fixx (4%; Thermo Electron, Pittsburgh, PA) >20 h and then subjected to decalcification in a solution containing 0.25 M Trizma base (Sigma) (17 (link)) for 14 days.
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8

Histomorphometric Analysis of Bone Maturation

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Callus formation and bone maturation were assessed by means of histomorphometric analysis of Movat pentachrome and osteocalcin immunostained decalcified sections taken from the bone defect. For histological evaluation of bone maturation, bones were carefully defrosted and fixed in Zinc-Formal-Fixx, 10% over 20 h (Thermo Electron, Pittsburgh, USA) followed by decalcification for 14 days in 0.25 M Trizma base (Sigma-Aldrich, Taufkirchen, Germany) and 10% EDTA (Sigma-Aldrich), pH-value 7.4. Decalcified bones were paraffin embedded; longitudinal Sections (3 µm) were taken. Movat pentachrome staining of paraffin embedded histological slides was performed as published by Garvey et al. [31 (link)] using a staining kit according to the manufacturer’s instructions (Morphisto, Frankfurt, Germany). All slides were analysed using light microscopy. High resolution images depicting the whole defect zone in each case were created by automated stitching of multiple single frames covering the whole defect using the software BZII Analyser (Keyence, Neu-Isenburg, Germany). New bone formation and cartilaginous tissue area were then analysed in the defect site using the software ImageJ (https://imagej.nih.gov/ij/) and the relative tissue positive area of the entire defect zone was calculated.
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9

Electrical Stimulation for Limb Regeneration

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Electrical stimulation was applied using a purpose-built bimetallic device and surgeries were performed as described previously32 (link). Animals were euthanized (CO2 inhalation) at 3-, 7- and 28- days post amputation, weighed, and the limb stumps were collected and carefully examined macro- and microscopically. In the macroscopic examination, the skin covering the limb stumps of the EStim and sham-treated animals was carefully incised and the EStim device and corresponding electrodes were controlled for integrity and carefully removed. In addition, all limbs were inspected for signs of infection and/or tumors. The specimens were fixed in Zinc-Formal-Fixx, (Thermo Electron, USA) for 24hrs and stored for subsequent histomorphometric and immunohistological analysis or stored in liquid nitrogen for subsequent RNA isolation.
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10

Histological Analysis of Femur Defects

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For histological analysis, femurs were defrosted and fixed in 10% Zinc-Formal-Fixx (Thermo Electron, Pittsburgh) for 20 h. Subsequently, decalcification in 0.25 M Trizma base (Sigma–Aldrich) and 10% EDTA, pH 7.4, followed. Decalcified femurs were paraffin embedded and cut in Sections (3 μm) parallel to their long axis. Movat's pentachrome staining was performed as described by Garvey et al. using a staining kit (Morphisto, Frankfurt, Germany) [25 (link)].
For evaluation, the periosteum regrowth from both sides into the defect was measured and given as the sum of distances from the right and left side. A value of 7000 µm, for example, means a regrowth of 3.5 mm from right and left fracture site into the defect, leaving a 3 mm gap.
Histomorphometric analysis was used to determine the extent of bone formation in the defect area. Using the polygon tool, the bony tissue within the defect boundaries was marked and the percentage of new bone to total defect area was calculated. The software ImageJ (https://imagej.nih.gov/ij/) was used. The location of new bone formation was evaluated purely descriptive.
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